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Welcome to the H. salinarum NRC-1 Atlas! In this web portal, you can explore a multi-omics growth curve experiment for this archaeal organism. Below, you will find an interactive table with linked locus tags that will take you to a single-nucleotide resolution genome browser displaying time point-wise transcriptome profiles and miscellaneous features for a given gene and its neighbors. You can also browse the data by visualizing an interactive heat map of all genes with their transcript and protein levels accompanied by miscellaneous features (“Atlas” tab). The “About” section provides a detailed description of this web portal. For the best user experience, please, use the Google Chrome Browser.

About

Table of contents

<WE NEED A TABLE OF CONTENTS HERE (TWO-LEVELS ARE ENOUGH). THIS IS AN EXTENSIVE DESCRIPTION PAGE>

Introduction

The H. salinarum NRC-1 Atlas is a web resource conceived to support the discovery of potential post-transcriptional regulation mechanisms by observing multi-omics data of a growth curve experiment and miscellaneous features obtained from public data. It debuted as a companion web portal for the manuscript entitled “A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon” (Lorenzetti et al., 2022). Below, we describe each section of this web portal.

Portal description

Home

The landing page for this web portal shows three searchable tables that can be activated by clicking on their respective tabs:

  • Locus tag: This table brings an index of the genes you can browse. Each row starts with a non-redundant representative open reading frame (column #1) followed by its symbol (column #2), its protein product (column #3), and a list of locus tags corresponding to (quasi)identical genes within the same annotation effort or coming from other resources (e.g., strain R1). If you need more details on how this non-redundant set of genes was generated, please, refer to H. salinarum NRC-1 non-redundant transcriptome resource;

  • COG Info: This table brings information retrieved from the clusters of orthologous genes (COG) database (Galperin, et al., 2021). For each representative open reading frame (column #1), we list the ID (column #2), the enunciate (column #3), the category (column #4), and the functional pathway (column #5);

  • IS Info: This table brings a non-redundant set of insertion sequences (mobile genetic elements). The open reading frames (column #1) are localized within the named insertion sequences (column #2) from various families (column #3) and subgroups (column #4).

Clicking on the linked locus tags will take you to a page dedicated to the selected gene. It should take about 30 seconds to load the page. There, you will get general information about the gene and a genome browser centering on the region of interest and its neighbors. Notice that you cannot go far right or left because the features will disappear after a few kilobases. That is a consequence of downsizing the data sets to avoid memory-related crashes. If you would like to browse another gene, please, go back to the “Home” section and start your search again.

All the genes can be explored using the genome browser, but not all will show miscellaneous information. Below, we list a set of features that can be displayed for a selected gene.

  • Annotations: The location following the format “replicon start end” (column #1); clusters of orthologous genes ID (column #2); possibly deprecated GenBank ID (column #3); gene symbol (column #4); <FROM WHERE?>

  • Genome Browser: This subsection displays an embedded genome browser window powered by igv.js. From top to bottom, the tracks are:

    • The nucleotide sequence and its three-frame translation (only visible when zoomed-in);

    • Ribo-Seq TP1-4 (+): Normalized read depth tracks for the ribosome profiling experiment (positive strand) sampled from four consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase). Mean of three replicates;

    • RNA-Seq TP1-4 (+): Normalized read depth tracks for the RNA-Seq experiment (positive strand) sampled from four consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase). Mean of three replicates;

    • TPS (+): Transcript processing sites (positive strand) collected from Ibrahim et al. (2021);

    • SmAP1 interaction (+): Protein-RNA interaction inferred from a SmAP1-RNA co-immunoprecipitation assay followed by next-generation sequencing (positive strand);

    • Antisense RNAs: Antisense RNA annotation from de Almeida et al. (2019);

    • Genes: Gene and coding sequence (CDS) annotation from Pfeiffer et al. (2019);

    • IS annotation: Insertion sequence annotation from Pfeiffer et al. (2019);

    • SmAP1 interaction (-): Protein-RNA interaction inferred from a SmAP1-RNA co-immunoprecipitation assay followed by next-generation sequencing (negative strand);

    • TPS (-): Transcript processing sites (negative strand) collected from Ibrahim et al. (2021);

    • Ribo-Seq TP1-4 (-): Normalized read depth tracks for the ribosome profiling experiment (negative strand) sampled from four consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase). Mean of three replicates;

    • RNA-Seq TP1-4 (-): Normalized read depth tracks for the RNA-Seq experiment (negative strand) sampled from four consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase). Mean of three replicates;

    • The user can choose whether raw or log-transformed read depth is displayed by unchecking/checking the box located at the top of the genome browser window; it is also possible to customize each track by clicking on the right-hand size gear button.

  • COG information: Information collected from the clusters of orthologous genes (COG) database (Galperin, et al., 2021);

  • Gene ontology: Information collected from <FROM WHERE?>;

  • Cross References: Links to multiple external resources;

  • Gene Regulatory Network: Links to environmental gene regulatory influence networks (EGRIN) databases;

  • Transcript Structure: Transcript structure for the target gene and its neighbors;

  • Data: Transcriptome levels measured by microarrays in multiple conditions for the selected gene;

  • Sequences: DNA and protein sequences for the selected gene.

Atlas

This tab displays an interactive heat map powered by InteractiveComplexHeatmap and Shiny R packages. It should take about 40 seconds to load the tool using the Google Chrome Browser. Once the device is loaded, the user should be able to browse a comprehensive heat map, including 2,579 protein coding entries (rows) of the H. salinarum NRC-1 genome grouped by COG categories. On the left-hand side, we displayed several annotation columns:

  • COG: Category according to the clusters of orthologous genes (COG) database (Galperin et al., 2021);

  • Chromosome: The representative instance is located within the chromosome (NC_002607.1);

  • pNRC100: The representative instance is located within the plasmid pNRC100 (NC_001869.1);

  • pNRC200: The representative instance is located within the plasmid pNRC200 (NC_002608.1);

  • SmAP1: Whether there is at least one SmAP1 binding site on the same strand for a given gene;

  • asRNA: Whether there is at least one annotated antisense RNA (asRNA) according to de Almeida et al. (2019);

  • TPS: Whether there is at least one transcript processing site (TPS) on the same strand for a given gene according to Ibrahim et al. (2021);

  • 2099: Log2-transformed fold change of RNase_2099C knockout vs. the control strain. Data reanalysis of Wurtmann et al. (2014);

  • Half-life: Experimentally determined half-life of a transcript according to Hundt et al. (2007);

  • CAI: Codon adaptation index computed using the 5% most abundant proteins in this study as the reference set;

  • GC Content: Difference (residue) between GC content for a given gene and the mean GC content considering all the genes.

Moreover, the tool shows five heat maps side-by-side, grouped by COG categories and clustered by Protein levels:

  • Protein: Log10-transformed proteome quantitative measure (a pseudocount was imputed for missing values) for consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase);

  • mRNA: Log10-transformed transcriptome quantitative measure (TPM+1) for consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase);

  • RPF: Log10-transformed ribosome mRNA protected fragment quantitative measure (RPF; Ribo-Seq experiment; TPM+1) for consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase);

  • TE: Log2-transformed translational efficiency for consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase). Given by Protein divided by mRNA in a time point-wise manner;

  • RO: Log2-transformed ribosome occupancy for consecutive time points of a growth curve (TP1: early exponential growth phase; TP2: mid-exponential growth phase; TP3: late exponential growth phase; TP4: stationary phase). Given by RPF divided by mRNA in a time point-wise manner.

Atlas (Static)

This is a static version of the same heat map displayed in the “Atlas” section. It should take about one minute to load the static heat map using the Google Chrome Browser. We realized that computers with old hardware and/or slow internet connections might be unable to load the interactive heat map successfully, so we built this static version. Please, see the download section below to download it as a PDF file.

Usage examples

Selecting a gene to open in the genome browser

Browsing the mobilome cluster using the interactive heat map

Using the interactive heat map search tool

For that, we are going to use a comma-separated set of locus tags for genes comprising the gvp cluster. Only representative locus tags are allowed (see column #1 in the table at the “Home” section for all the possible entries).

VNG_7015,VNG_7016,VNG_7017,VNG_7018,VNG_7019,VNG_7020,VNG_7021,VNG_7022,VNG_7023,VNG_7024,VNG_7025,VNG_7026,VNG_7027,VNG_7028

Downloading data for the gvp gene cluster demonstrated above

Data download

You can download data for the following:

  • Atlas: The entire table used to generate the interactive heat map is available here and as a supplement file in our manuscript (protein levels, RNA-Seq levels, Ribo-Seq levels, translational efficiency, and ribosome occupancy are not log-transformed in this version; the column description is available inside the workbook);

  • Atlas (Static): A PDF file for the static heat map is available here;

  • Genome browser: A bundle containing all the tracks is available here. We identify each file below, and you should be able to get more details each track in the genome browser description above:

    • Hsalinarum.fa: Halobacterium salinarum NRC-1 genome sequence (FASTA format);

    • Hsalinarum.fa.fai: FASTA index for the genome sequence file;

    • Hsalinarum-gene-annotation-pfeiffer2019-adjusted-names.gff3: Gene annotation file (GFF3);

    • Hsalinarum-846asRNAs-deAlmeida2019.gff3: Antisense RNA annotation (GFF3);

    • Hsalinarum-pfeiffer2019-mobileElements.gff3: Insertion sequence annotation (GFF3);

    • mergedBRs_interaction-regions-entire-genome-[fr][we][dv].gff3: SmAP1 interaction regions (GFF3) for the positive and negative strands (fwd and rev, respectively);

    • TPS_gff_[fr][we][dv].gff3: Transcript processing sites (GFF3) for the positive and negative strands (fwd and rev, respectively);

    • ribosomal_RNA_TP[1234]-[fr][we][dv].bedgraph: Ribo-Seq read depth for samples obtained from consecutive time points of a growth curve (TP1-4). Positive and negative strands are represented by fwd and rev, respectively (BEDGRAPH format);

    • total-RNA-TP[1234]-[fr][we][dv].bedgraph: RNA-Seq read depth for samples obtained from consecutive time points of a growth curve (TP1-4). Positive and negative strands are represented by rev and fwd, respectively (BEDGRAPH format). Notice rev and fwd are inverted here, since the sequencing libraries were prepared using the TruSeq mRNA Stranded kit (Illumina).

Citation

If you make use of this web portal or the data we made public, please, cite:

Lorenzetti et al. (2022). “A genome-scale atlas reveals complex interplay of transcription and translation in an archaeon“. Journ. Nam., X(n), XX-XX.

Bugs and feature requests

The code for this web portal is publicly available on GitHub. Please, leave your bug reports, suggestions, and feature requests here.